The Obama administration is preparing for the prospect that Islamist governments will take hold in North Africa and the Middle East, acknowledging that the popular revolutions there will bring a more religious cast to the region's politics.

The administration is already taking steps to distinguish between various movements in the region that promote Islamic law in government. An internal assessment, ordered by the White House last month, identified large ideological differences between such movements as the Muslim Brotherhood in Egypt and al-Qaeda that will guide the U.S. approach to the region.

"We shouldn't be afraid of Islam in the politics of these countries," said a senior administration official, speaking on the condition of anonymity to describe internal policy deliberations. "It's the behavior of political parties and governments that we will judge them on, not their relationship with Islam."

Islamist governments span a range of ideologies and ambitions, from the primitive brutality of the Taliban in Afghanistan to Turkey's Justice and Development Party, a movement with Islamist roots that heads a largely secular political system.

None of the revolutions over the past several weeks has been overtly Islamist, but there are signs that the uprisings could give way to more religious forces. An influential Yemeni cleric called this week for the U.S.-backed administration of President Ali Abdullah Saleh to be replaced with Islamist rule, and in Egypt, an Islamist theoretician has a leading role in drafting constitutional changes after President Hosni Mubarak's fall from power last month.

A number of other Islamist parties are deciding now how big a role to play in protests or post-revolution reforms.

Since taking office, President Obama has argued for a "new beginning" with Islam, suggesting that Islamic belief and democratic politics are not incompatible. But in doing so, he has alarmed some foreign-policy pragmatists and allies such as Israel, who fear that governments based on religious law will inevitably undercut democratic reforms and other Western values.

Some within the U.S. intelligence community, foreign diplomatic circles and the Republican Party say Obama's readiness to accept Islamist movements, even ones that meet certain conditions, fails to take into consideration the methodical approach many such parties adopt toward gradually transforming secular nations into Islamic states at odds with U.S. policy goals.

Hezbollah in Lebanon and Hamas in the Palestinian territories have prospered in democratic elections and exert huge influence. Neither party, each with an armed wing, supports Israel's right to exist, nor have they renounced violence as a political tool.

And while many in the region point to Turkey as a model mixture of Islam and democracy, the ruling Islamist party is restrained by the country's highly secular army and court system, a pair of strong institutional checks that countries such as Egypt and Tunisia lack.

"The actual word and definition of Islamism does not in and of itself pose a threat," said Jonathan Peled, the spokesman for the Israeli Embassy in Washington, citing Israel's relationship with the Turkish government, among others.

But Peled said Israel fears that "anti-democratic extremist forces could take advantage of a democratic system," as, he said, Hamas did with its 2006 victory in Palestinian parliamentary elections. Israel allowed Hamas to participate only under pressure from the George W. Bush administration as part of its stated commitment to promote Arab democracy.

"We obviously have concerns that are different than the administration's," Peled said. "We live in the neighborhood, obviously, and so we experience the results more closely."

The choice between stability and democracy has been a constant tension in U.S. foreign policy, and in few places has it been more pronounced than in the Middle East.

Many of the fallen or imperiled autocrats in the region were supported by successive U.S. governments, either as Cold War foils to the Soviet Union or as bulwarks against Islamist extremism before and after the Sept. 11, 2001, attacks.

In his June 2009 address at Cairo University, Obama acknowledged the controversy that the Bush administration's democracy promotion stirred in the region.

"That does not lessen my commitment, however, to governments that reflect the will of the people," he said, adding that "each nation gives life to the principle in its own way, grounded in the traditions of its own people."

In the Arab Middle East, those traditions include Islam, although Obama did not directly address the religion's role in democratic politics. He said the United States "will welcome all elected, peaceful governments - provided they govern with respect for all their people."

The goal of Islamist movements after taking power is at the root of concern expressed by Republican lawmakers and others in Washington.

Paul Pillar, a longtime CIA analyst who now teaches at Georgetown University, said, "Most of the people in the intelligence community would see things on this topic very similarly to the president - that is, political Islam as a very diverse series of ideologies, all of which use a similar vocabulary, but all quite different."

"The main challenge President Obama will face is a political challenge from across the aisle, and one reinforced by Israel," said Pillar, whose portfolio included the Middle East.

As the Arab revolutions unfold, the White House is studying various Islamist movements, identifying ideological differences for clues to how they might govern in the short and long term.

The White House's internal assessment, dated Feb. 16, looked at the Muslim Brotherhood's and al-Qaeda's views on global jihad, the Israeli-Palestinian conflict, the United States, Islam in politics, democracy and nationalism, among others.

The report draws sharp distinctions between the ambitions of the two groups, suggesting that the Brotherhood's mix of Islam and nationalism make it a far different organization than al-Qaeda, which sees national boundaries as obstacles to restoring the Islamic caliphate.

The study also concludes that the Brotherhood criticizes the United States largely for what it perceives as America's hypocritical stance toward democracy - promoting it rhetorically but supporting leaders such as Mubarak.

"If our policy can't distinguish between al-Qaeda and the Muslim Brotherhood, we won't be able to adapt to this change," the senior administration official said. "We're also not going to allow ourselves to be driven by fear."

After Hamas won the Palestinian parliamentary elections in 2006, the United States and Israel led an international boycott of the government. But Obama administration officials, reviewing that history with an eye toward the current revolutions, say the reason for the U.S. boycott was not Hamas's Islamic character but its refusal to agree to conditions such as recognizing Israel.

In a speech Monday in Geneva, Secretary of State Hillary Rodham Clinton appeared to draw on that lesson, implicitly inviting Islamist parties to participate in the region's future elections with conditions. "Political participation," Clinton said, "must be open to all people across the spectrum who reject violence, uphold equality and agree to play by the rules of democracy."

It appears that the US Administration is caught between the Devil and the Deep Sea and has to accept the situation as pragmatically as feasible.

There is indeed a danger that the AQ type of radical fundamentalists may use the popular support and hijack it for radical regimes that recognises nothing beyond Islam. That would be a dangerous situation.

To believe that Islam would not play a role in the Arab world if democracy comes, would be too naive. It is the autocratic regimes who have been able to control radical Islamic fundamentalist of the AQ flavour from flourishing and now the time has come for such autocratic regime being shown the door.

Therefore, if Islamic overtones in Arab democracies cannot be avoided, it is better to have the benign variety than the fundamental radicalism signatured by the AQ.

Much of the radicalization has come from USA indirectly, 2 wars Iraq and Afghanistan, possible conflict in Iran ,warships and troops now in Libya, drone attacks in Pakistan. All this can be viewed (misunderstood??) as wars against muslims.